void readBenchmarkGeneList(string benchmarkGeneListFilename, vector<int>* cancerBenchmarkGenes, map<string, int>* geneSymbolToId){
ifstream inFile;
inFile.open(benchmarkGeneListFilename.c_str(), std::ifstream::in);
map<string, int>::iterator end = geneSymbolToId->end();
if (inFile.is_open()) {
//for each row
while (inFile.good()) {
string s;
if (!getline(inFile, s))
break;
istringstream rowStr(s);
int i = 0;
bool found = false;
while (rowStr) { //for each column
string s;
if (!getline(rowStr, s, '\t'))
break;
if(i == 0){ //read gene symbols at the first column
//trim the whitespace at the end of the string
s.erase(s.find_last_not_of(" \n\r\t")+1);
map<string, int>::iterator it = geneSymbolToId->find(s);
if(it != end){ //found in the network
found = true;
cancerBenchmarkGenes->push_back(it->second); //add the gene id to geneEx
// cout << s << endl;
}else{
found = false;
// cout << s << " not found" << endl;
}
}
else if(i == 7){ //read tumor type (somatic mutation)
}
if(!found) //not found in the network, so skip this row (gene)
break;
i++; //go to the next column (sample)
}
}
inFile.close();
} else {
cerr << "Error opening file\n";
}
}
Island::Island(const std::string& filename, int pos_x, int pos_y, std::vector<bool>& waterTiles) : m_x(pos_x), m_y(pos_y), m_tiles(NULL), m_defaultTile(0)
{
m_defaultTile = Tile::getDefaultTile();
std::cout << "Trying to load island \"" << filename << "\"" << std::endl;
TiXmlDocument document;
if (!document.PHYSFS_LoadFile(filename))
{
throw FileLoadException(filename, document.ErrorDesc());
}
if(!document.RootElement() || document.RootElement()->ValueStr() != "island")
throw XMLException(filename, -1, "This is no valid island XML file (missing island root element)");
TiXmlElement *island = document.RootElement();
if (!island->Attribute("cols"))
throw XMLException(filename, island->Row(), "Missing attribute cols");
if (!island->Attribute("rows"))
throw XMLException(filename, island->Row(), "Missing attribute rows");
if (!island->Attribute("clime"))
throw XMLException(filename, island->Row(), "Missing attribute clime");
std::stringstream attr;
attr << island->Attribute("cols") << " " << island->Attribute("rows");
attr >> m_cols >> m_rows;
m_clime = island->Attribute("clime");
std::cout << "Creating " << (m_rows * m_cols) << " tiles" << std::endl;
m_tiles = new Tile* [m_rows * m_cols];
memset(m_tiles, 0, sizeof(Tile*) * m_rows * m_cols);
TiXmlElement *terrain = island->FirstChildElement("terrain");
if (!terrain)
throw XMLException(filename, island->Row(), "Missing toplevel element terrain");
TiXmlElement *row = terrain->FirstChildElement("row");
if (!terrain)
throw XMLException(filename, terrain->Row(), "Missing row subelements");
while (row)
{
if (!row->Attribute("value"))
throw XMLException(filename, row->Row(), "Missing attribute value");
std::stringstream rowStr(row->Attribute("value"));
int rowInt;
rowStr >> rowInt;
rowInt--;
TiXmlElement *col = row->FirstChildElement("col");
if (!col)
throw XMLException(filename, row->Row(), "Missing col subelements");
while (col)
{
if (!col->Attribute("value"))
throw XMLException(filename, col->Row(), "Missing attribute value");
std::stringstream colStr(col->Attribute("value"));
int colInt;
colStr >> colInt;
colInt--;
TiXmlElement *tile = col->FirstChildElement("tile");
if (!tile)
throw XMLException(filename, col->Row(), "Missing tile subelement");
if (((rowInt * m_cols) + colInt) >= m_cols * m_rows)
std::cout << "WARNING! Index out of bounds. Row: " << rowInt << ", column: " << colInt << std::endl;
else
{
m_tiles[(rowInt * m_cols) + colInt] = new Tile(tile);
if (m_tiles[(rowInt * m_cols) + colInt] == NULL) {
std::cout << "TILE CREATION FAILED" << std::endl;
}
waterTiles[(rowInt * m_cols) + colInt] = false;
}
col = col->NextSiblingElement("col");
}
row = row->NextSiblingElement("row");
}
std::cout << "Succesfully loaded island \"" << filename << "\"" << std::endl;
std::cout << "\tColums: " << m_cols << std::endl;
std::cout << "\tRows: " << m_rows << std::endl;
/* std::cout << "debug-listing 0,0 to 9,9" << std::endl;
for (int y = 0; y < 10; y++)
{
for (int x = 0; x < 10; x++)
{
std::cout << m_tiles[(y * m_cols) + x]->getName();
std::cout << ",";
}
std::cout << std::endl;
}*/
}
